Consistent, the same alleles at the same sites were determined by both the chip and resequencing methods; Heterozygous > homozygous, heterozygotes called on the chip were under-called as homozygote with one identical allele in the resequencing pipelines; As indels, SNP sites on the chip were called as indels in resequencing pipelines; Inconsistent, heterozygous calls with the chip and resequencing pipelines but with different alleles.